One way to damage a bore is to use a bore brush that is harder then the barrel metal. That is why we almost never use Stainless bore brushes. With nylon or brass brushes, it is impossible to damage the bore unless you are running metal shaving or sand in with the brush.
As long as you keep your gear clean and use a bore guide, it is pretty much impossible to damage a bore using contemporary cleaners and cleaning equipment.
If you are experiencing heavy fouling, try strong cleaners like Barnes CR10. If your bore is rough, consider hand lapping with JB non embedding compound or their lapping rouge.
If instructions are followed, you can't damage your barrel. Remember that no matter how much effort you put behind that rod, you will never equal the 50,000PSI of burning powder and moving bullet.